NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|15597954|ref|NP_251448|]
View 

transcriptional regulator [Pseudomonas aeruginosa PAO1]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

LysR family transcriptional regulator containing an N-terminal HTH (helix-turn-helix) DNA-binding domain and a C-terminal substrate binding domain, which is structurally homologous to the type 2 periplasmic-binding (PBP2) fold proteins

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0003677|GO:0006355
PubMed:  19047729|8257110|15808743
SCOP:  4000316

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
8-293 2.96e-45

DNA-binding transcriptional regulator, LysR family [Transcription];


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 153.48  E-value: 2.96e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954   8 IELFLAVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERTHREARPTALARALAPQARMIAEQLAQLQVHALEL 87
Cdd:COG0583   6 LRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRAL 85

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954  88 SQGLESRLSLGVVADIDSGRLFGALRTLSERYPLLDVEVLSAAQDDALALLHGGRISLCFGFAgisvnpqerfqyvgaes 167
Cdd:COG0583  86 RGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLG----------------- 148

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954 168 lvatiSPRHPALQkpGQALYLEELVnvrqiLVASCDLPLADTRPLiagacwrTDSLGTALEMVEAGIGWGNFPLSRVAPL 247
Cdd:COG0583 149 -----PPPDPGLV--ARPLGEERLV-----LVASPDHPLARRAPL-------VNSLEALLAAVAAGLGIALLPRFLAADE 209

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*.
gi 15597954 248 LATGRLVRLDFRNTknELKLPVHAIWLKNQPLRKAAQELVGMLATR 293
Cdd:COG0583 210 LAAGRLVALPLPDP--PPPRPLYLVWRRRRHLSPAVRAFLDFLREA 253
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
8-293 2.96e-45

DNA-binding transcriptional regulator, LysR family [Transcription];


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 153.48  E-value: 2.96e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954   8 IELFLAVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERTHREARPTALARALAPQARMIAEQLAQLQVHALEL 87
Cdd:COG0583   6 LRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRAL 85

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954  88 SQGLESRLSLGVVADIDSGRLFGALRTLSERYPLLDVEVLSAAQDDALALLHGGRISLCFGFAgisvnpqerfqyvgaes 167
Cdd:COG0583  86 RGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLG----------------- 148

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954 168 lvatiSPRHPALQkpGQALYLEELVnvrqiLVASCDLPLADTRPLiagacwrTDSLGTALEMVEAGIGWGNFPLSRVAPL 247
Cdd:COG0583 149 -----PPPDPGLV--ARPLGEERLV-----LVASPDHPLARRAPL-------VNSLEALLAAVAAGLGIALLPRFLAADE 209

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*.
gi 15597954 248 LATGRLVRLDFRNTknELKLPVHAIWLKNQPLRKAAQELVGMLATR 293
Cdd:COG0583 210 LAAGRLVALPLPDP--PPPRPLYLVWRRRRHLSPAVRAFLDFLREA 253
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 94-293 1.55e-21

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 90.04  E-value: 1.55e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954    94 RLSLGVVADIDSGRLFGALRTLSERYPLLDVEVLSAAQDDALALLHGGRISLCFGFaGISVNPQERFQYVGAESLVATIS 173
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRR-GPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954   174 PRHPALQkpGQALYLEELVNVRQILVAscdlPLADTRPLIAGAC----------WRTDSLGTALEMVEAGIGWGNFPLSR 243
Cdd:pfam03466  82 PDHPLAR--GEPVSLEDLADEPLILLP----PGSGLRDLLDRALraaglrprvvLEVNSLEALLQLVAAGLGIALLPRSA 155

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 15597954   244 VAPLLATGRLVRLDFRNTknELKLPVHAIWLKNQPLRKAAQELVGMLATR 293
Cdd:pfam03466 156 VARELADGRLVALPLPEP--PLPRELYLVWRKGRPLSPAVRAFIEFLREA 203
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 94-290 6.81e-17

The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, oxidative stress responses, nodule formation of nitrogen-fixing bacteria, synthesis of virulence factors, toxin production, attachment and secretion, to name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 77.26  E-value: 6.81e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954  94 RLSLGVVADIDSGRLFGALRTLSERYPLLDVEVLSAAQDDALALLHGGRIslCFGFAGISVNPQE-RFQYVGAESLVATI 172
Cdd:cd05466   1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGEL--DLAIVALPVDDPGlESEPLFEEPLVLVV 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954 173 SPRHPALQKPgqALYLEELVNVRQILVASCDlplaDTRPLIAGACW----------RTDSLGTALEMVEAGIGWGNFPlS 242
Cdd:cd05466  79 PPDHPLAKRK--SVTLADLADEPLILFERGS----GLRRLLDRAFAeagftpnialEVDSLEAIKALVAAGLGIALLP-E 151

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*...
gi 15597954 243 RVAPLLATGRLVRLDFRNTknELKLPVHAIWLKNQPLRKAAQELVGML 290
Cdd:cd05466 152 SAVEELADGGLVVLPLEDP--PLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 3-256 8.35e-15

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 73.05  E-value: 8.35e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954    3 FSSDTIELFLAVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERTHREARPTALARALAPQARMIAEQLAQLQV 82
Cdd:PRK11074   2 WSEYSLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954   83 HALELSQGLESRLSLGV------------VADIdsgrlfgaLRTLSERYPLLDVEVLSAAQdDALAllhGGRISLCFG-F 149
Cdd:PRK11074  82 QCQQVANGWRGQLSIAVdnivrpdrtrqlIVDF--------YRHFDDVELIIRQEVFNGVW-DALA---DGRVDIAIGaT 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954  150 AGISVNPQERFQYVGAESLVATISPRHPALQKPGqALYLEELVNVRQILV--ASCDLPLADT------RPLIAGAcWRtd 221
Cdd:PRK11074 150 RAIPVGGRFAFRDMGMLSWACVVSSDHPLASMDG-PLSDDELRPYPSLCLedTSRTLPKRITwlldnqRRLVVPD-WE-- 225

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 15597954  222 slgTALEMVEAGIGWGNFPLSRVAPLLATGRLVRL 256
Cdd:PRK11074 226 ---SAINCLSAGLCVGMVPTHFAKPLINSGKLVEL 257
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 11-257 1.17e-13

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 69.56  E-value: 1.17e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954    11 FLAVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERThREARPTALARAL---APQARMI-AEQLAQLQVHAle 86
Cdd:TIGR03298   9 LAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVRT-QPCRATEAGQRLlrhARQVRLLeAELLAELPGLA-- 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954    87 lsQGLESRLSLGVVADIDSGRLFGALRTLSERYPLLdVEVLSAAQDDALALLHGGRISLCfgfagISVNPQE----RFQY 162
Cdd:TIGR03298  86 --PGAPTRLTIAVNADSLATWFLPALAPVLAREGVL-LDLVVEDQDHTAELLRSGEVLGA-----VTTEAKPvpgcRVVP 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954   163 VGAESLVATISPRHpalqkpgQALYLEELVNVRQILVASC-------DLPLADTRPLIAGA----CWRTDSLGTALEMVE 231
Cdd:TIGR03298 158 LGAMRYLAVASPAF-------AARYFPDGVTAAALARAPVivfnrkdDLQDRFLRRLFGLPvsppRHYVPSSEGFVDAAR 230

                         250       260
                  ....*....|....*....|....*.
gi 15597954   232 AGIGWGNFPLSRVAPLLATGRLVRLD 257
Cdd:TIGR03298 231 AGLGWGMVPELQAEPHLAAGRLVELA 256
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-290 2.12e-12

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 66.10  E-value: 2.12e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954    1 MNFSSdtIELFLAVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERTHREARPTALARALAPQAR-MIAEQlaQ 79
Cdd:NF040786   1 MNLKQ--LEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKeMLDLW--E 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954   80 LQVHALELSQGLESR-LSLGVVADIDSGRLFGALRTLSERYPLLDVEVLSAAQDDALALLHGGRISlcFGFAGISVNpQE 158
Cdd:NF040786  77 KLEEEFDRYGKESKGvLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVD--IGFTGTKLE-KK 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954  159 RFQY--VGAESLVATISPRHPALQKPGQALYLEELVNVRQIL--------------VASCDLPLADTRpLIAgacwRTDS 222
Cdd:NF040786 154 RLVYtpFYKDRLVLITPNGTEKYRMLKEEISISELQKEPFIMreegsgtrkeaekaLKSLGISLEDLN-VVA----SLGS 228

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15597954  223 LGTALEMVEAGIGWGnFpLSR--VAPLLATGRLVRLDFRNtknelkLPV----HAIWLKNQPLRKAAQELVGML 290
Cdd:NF040786 229 TEAIKQSVEAGLGIS-V-ISElaAEKEVERGRVLIFPIPG------LPKnrdfYLVYNKNRQLSPTAEAFLQFV 294
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
8-293 2.96e-45

DNA-binding transcriptional regulator, LysR family [Transcription];


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 153.48  E-value: 2.96e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954   8 IELFLAVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERTHREARPTALARALAPQARMIAEQLAQLQVHALEL 87
Cdd:COG0583   6 LRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRAL 85

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954  88 SQGLESRLSLGVVADIDSGRLFGALRTLSERYPLLDVEVLSAAQDDALALLHGGRISLCFGFAgisvnpqerfqyvgaes 167
Cdd:COG0583  86 RGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLG----------------- 148

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954 168 lvatiSPRHPALQkpGQALYLEELVnvrqiLVASCDLPLADTRPLiagacwrTDSLGTALEMVEAGIGWGNFPLSRVAPL 247
Cdd:COG0583 149 -----PPPDPGLV--ARPLGEERLV-----LVASPDHPLARRAPL-------VNSLEALLAAVAAGLGIALLPRFLAADE 209

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*.
gi 15597954 248 LATGRLVRLDFRNTknELKLPVHAIWLKNQPLRKAAQELVGMLATR 293
Cdd:COG0583 210 LAAGRLVALPLPDP--PPPRPLYLVWRRRRHLSPAVRAFLDFLREA 253
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 94-293 1.55e-21

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 90.04  E-value: 1.55e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954    94 RLSLGVVADIDSGRLFGALRTLSERYPLLDVEVLSAAQDDALALLHGGRISLCFGFaGISVNPQERFQYVGAESLVATIS 173
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRR-GPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954   174 PRHPALQkpGQALYLEELVNVRQILVAscdlPLADTRPLIAGAC----------WRTDSLGTALEMVEAGIGWGNFPLSR 243
Cdd:pfam03466  82 PDHPLAR--GEPVSLEDLADEPLILLP----PGSGLRDLLDRALraaglrprvvLEVNSLEALLQLVAAGLGIALLPRSA 155

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 15597954   244 VAPLLATGRLVRLDFRNTknELKLPVHAIWLKNQPLRKAAQELVGMLATR 293
Cdd:pfam03466 156 VARELADGRLVALPLPEP--PLPRELYLVWRKGRPLSPAVRAFIEFLREA 203
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 94-290 6.81e-17

The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, oxidative stress responses, nodule formation of nitrogen-fixing bacteria, synthesis of virulence factors, toxin production, attachment and secretion, to name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 77.26  E-value: 6.81e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954  94 RLSLGVVADIDSGRLFGALRTLSERYPLLDVEVLSAAQDDALALLHGGRIslCFGFAGISVNPQE-RFQYVGAESLVATI 172
Cdd:cd05466   1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGEL--DLAIVALPVDDPGlESEPLFEEPLVLVV 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954 173 SPRHPALQKPgqALYLEELVNVRQILVASCDlplaDTRPLIAGACW----------RTDSLGTALEMVEAGIGWGNFPlS 242
Cdd:cd05466  79 PPDHPLAKRK--SVTLADLADEPLILFERGS----GLRRLLDRAFAeagftpnialEVDSLEAIKALVAAGLGIALLP-E 151

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*...
gi 15597954 243 RVAPLLATGRLVRLDFRNTknELKLPVHAIWLKNQPLRKAAQELVGML 290
Cdd:cd05466 152 SAVEELADGGLVVLPLEDP--PLSRTIGLVWRKGRYLSPAARAFLELL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
8-64 3.06e-16

Bacterial regulatory helix-turn-helix protein, lysR family;


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 71.26  E-value: 3.06e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 15597954     8 IELFLAVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERTHREARPTALAR 64
Cdd:pfam00126   4 LRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 3-256 8.35e-15

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 73.05  E-value: 8.35e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954    3 FSSDTIELFLAVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERTHREARPTALARALAPQARMIAEQLAQLQV 82
Cdd:PRK11074   2 WSEYSLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954   83 HALELSQGLESRLSLGV------------VADIdsgrlfgaLRTLSERYPLLDVEVLSAAQdDALAllhGGRISLCFG-F 149
Cdd:PRK11074  82 QCQQVANGWRGQLSIAVdnivrpdrtrqlIVDF--------YRHFDDVELIIRQEVFNGVW-DALA---DGRVDIAIGaT 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954  150 AGISVNPQERFQYVGAESLVATISPRHPALQKPGqALYLEELVNVRQILV--ASCDLPLADT------RPLIAGAcWRtd 221
Cdd:PRK11074 150 RAIPVGGRFAFRDMGMLSWACVVSSDHPLASMDG-PLSDDELRPYPSLCLedTSRTLPKRITwlldnqRRLVVPD-WE-- 225

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 15597954  222 slgTALEMVEAGIGWGNFPLSRVAPLLATGRLVRL 256
Cdd:PRK11074 226 ---SAINCLSAGLCVGMVPTHFAKPLINSGKLVEL 257
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 11-257 1.17e-13

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 69.56  E-value: 1.17e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954    11 FLAVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERThREARPTALARAL---APQARMI-AEQLAQLQVHAle 86
Cdd:TIGR03298   9 LAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVRT-QPCRATEAGQRLlrhARQVRLLeAELLAELPGLA-- 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954    87 lsQGLESRLSLGVVADIDSGRLFGALRTLSERYPLLdVEVLSAAQDDALALLHGGRISLCfgfagISVNPQE----RFQY 162
Cdd:TIGR03298  86 --PGAPTRLTIAVNADSLATWFLPALAPVLAREGVL-LDLVVEDQDHTAELLRSGEVLGA-----VTTEAKPvpgcRVVP 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954   163 VGAESLVATISPRHpalqkpgQALYLEELVNVRQILVASC-------DLPLADTRPLIAGA----CWRTDSLGTALEMVE 231
Cdd:TIGR03298 158 LGAMRYLAVASPAF-------AARYFPDGVTAAALARAPVivfnrkdDLQDRFLRRLFGLPvsppRHYVPSSEGFVDAAR 230

                         250       260
                  ....*....|....*....|....*.
gi 15597954   232 AGIGWGNFPLSRVAPLLATGRLVRLD 257
Cdd:TIGR03298 231 AGLGWGMVPELQAEPHLAAGRLVELA 256
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
9-256 5.04e-13

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 68.07  E-value: 5.04e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954    9 ELFLAVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERThREARPTALARALAPQARMIAEQLAQLQVHALELS 88
Cdd:PRK13348   8 EALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLRHLRQVALLEADLLSTLPAER 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954   89 QGLEsRLSLGVVADIDSGRLFGALRTLSERYPLLdVEVLSAAQDDALALLHGGRISLCfgfagISVNPQE---------- 158
Cdd:PRK13348  87 GSPP-TLAIAVNADSLATWFLPALAAVLAGERIL-LELIVDDQDHTFALLERGEVVGC-----VSTQPKPmrgclaeplg 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954  159 --RFQYVGAESLVATISP----RHPALQKPG---------QALYLEELVNVRQILVASCDLPladtrpliagacwRTDSL 223
Cdd:PRK13348 160 tmRYRCVASPAFAARYFAqgltRHSALKAPAvafnrkdtlQDSFLEQLFGLPVGAYPRHYVP-------------STHAH 226

                        250       260       270
                 ....*....|....*....|....*....|...
gi 15597954  224 GTALEMveaGIGWGNFPLSRVAPLLATGRLVRL 256
Cdd:PRK13348 227 LAAIRH---GLGYGMVPELLIGPLLAAGRLVDL 256
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-290 2.12e-12

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 66.10  E-value: 2.12e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954    1 MNFSSdtIELFLAVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERTHREARPTALARALAPQAR-MIAEQlaQ 79
Cdd:NF040786   1 MNLKQ--LEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKeMLDLW--E 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954   80 LQVHALELSQGLESR-LSLGVVADIDSGRLFGALRTLSERYPLLDVEVLSAAQDDALALLHGGRISlcFGFAGISVNpQE 158
Cdd:NF040786  77 KLEEEFDRYGKESKGvLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVD--IGFTGTKLE-KK 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954  159 RFQY--VGAESLVATISPRHPALQKPGQALYLEELVNVRQIL--------------VASCDLPLADTRpLIAgacwRTDS 222
Cdd:NF040786 154 RLVYtpFYKDRLVLITPNGTEKYRMLKEEISISELQKEPFIMreegsgtrkeaekaLKSLGISLEDLN-VVA----SLGS 228

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15597954  223 LGTALEMVEAGIGWGnFpLSR--VAPLLATGRLVRLDFRNtknelkLPV----HAIWLKNQPLRKAAQELVGML 290
Cdd:NF040786 229 TEAIKQSVEAGLGIS-V-ISElaAEKEVERGRVLIFPIPG------LPKnrdfYLVYNKNRQLSPTAEAFLQFV 294
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
3-254 5.43e-12

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 65.21  E-value: 5.43e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954    3 FSSDTIELFLAVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERTHREARPTALARALAPQARMIAEQLAQLQV 82
Cdd:PRK10094   2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPS 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954   83 HALELSQGLESRLSLgVVADI-----DSGRLfgaLRTLSERYPL----LDVEVLSAAQDdalALLHGGrISLCFGFAG-- 151
Cdd:PRK10094  82 ELQQVNDGVERQVNI-VINNLlynpqAVAQL---LAWLNERYPFtqfhISRQIYMGVWD---SLLYEG-FSLAIGVTGte 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954  152 -----ISVNPqerfqyVGAESLVATISPRHPALQKPG----QALYLEELVNVRqilvascdlplaDT-RPLIAGACWR-- 219
Cdd:PRK10094 154 alantFSLDP------LGSVQWRFVMAADHPLANVEEplteAQLRRFPAVNIE------------DSaRTLTKRVAWRlp 215

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 15597954  220 ------TDSLGTALEMVEAGIGWGNFPLSRVAPLLATGRLV 254
Cdd:PRK10094 216 gqkeiiVPDMETKIAAHLAGVGIGFLPKSLCQSMIDNQQLV 256
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
6-257 6.49e-12

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 64.79  E-value: 6.49e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954    6 DTIELFLAVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERThREARPTALARALAPQARmiaeQLAQLQ---V 82
Cdd:PRK03635   5 KQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGQRLLRHAR----QVRLLEaelL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954   83 HALELSQGLESRLSLGVVADIDSGRLFGALRTLSERYPLLdVEVLSAAQDDALALLHGGRIslcfgFAGISVNPQE---- 158
Cdd:PRK03635  80 GELPALDGTPLTLSIAVNADSLATWFLPALAPVLARSGVL-LDLVVEDQDHTAELLRRGEV-----VGAVTTEPQPvqgc 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954  159 RFQYVGAESLVATISPRHpalqkpgQALYLEELVNVRQILVASC-------DLP---LADTRPLIAGAcWRTDSLGTA-- 226
Cdd:PRK03635 154 RVDPLGAMRYLAVASPAF-------AARYFPDGVTAEALAKAPAvvfnrkdDLQdrfLRQAFGLPPGS-VPCHYVPSSea 225

                        250       260       270
                 ....*....|....*....|....*....|..
gi 15597954  227 -LEMVEAGIGWGNFPLSRVAPLLATGRLVRLD 257
Cdd:PRK03635 226 fVRAALAGLGWGMIPELQIEPELASGELVDLT 257
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
11-128 1.22e-09

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 58.09  E-value: 1.22e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954   11 FLAVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERTHREARPT--------ALARALapqarmiaEQLAQ--L 80
Cdd:PRK10086  22 FEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTeegkrvfwALKSSL--------DTLNQeiL 93

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 15597954   81 QVHALELSqgleSRLSLGVVADIDSGRLFGALRTLSERYPLLDVEVLS 128
Cdd:PRK10086  94 DIKNQELS----GTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILT 137
PRK09986 PRK09986
LysR family transcriptional regulator;
11-235 2.95e-09

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 56.65  E-value: 2.95e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954   11 FLAVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERTHREARPTALARALAPQARMIAEQLAQLQVHALELSQG 90
Cdd:PRK09986  15 FLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARVEQIGRG 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954   91 LESRLSLGVVADIDSGRLFGALRTLSERYPLLDVEVLSAAQDDALALLHGGRISLCFG-FAGISVNPQERFQYVGAESLV 169
Cdd:PRK09986  95 EAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWrMADLEPNPGFTSRRLHESAFA 174

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15597954  170 ATISPRHPALQKPgqALYLEELVNVRQILVAS--CDLPL--------ADTRPLIAgacWRTDSLGTALEMVEAGIG 235
Cdd:PRK09986 175 VAVPEEHPLASRS--SVPLKALRNEYFITLPFvhSDWGKflqrvcqqAGFSPQII---RQVNEPQTVLAMVSMGIG 245
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 8-233 2.47e-08

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 54.19  E-value: 2.47e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954    8 IELFLAVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERTHREARPTALARALAPQARMIAEQL--AQLQVH-A 84
Cdd:PRK11242   6 IRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLeaGRRAIHdV 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954   85 LELSQGlesRLSLGVVADIdSGRLFGAL-RTLSERYPLLDVEVLSAAQDDALALLHGGRISLCFGFAGISvNPQERFQYV 163
Cdd:PRK11242  86 ADLSRG---SLRLAMTPTF-TAYLIGPLiDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVH-SPEIEAQPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954  164 GAESLVATISPRHPALQKPgQALYLEELVNVRQILVAscdlPLADTRPLIAGACWR----------TDSLGTALEMVEAG 233
Cdd:PRK11242 161 FTETLALVVGRHHPLAARR-KALTLDELADEPLVLLS----AEFATREQIDRYFRRhgvtprvaieANSISAVLEIVRRG 235
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 94-235 3.57e-07

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176106 [Multi-domain]  Cd Length: 197  Bit Score: 49.43  E-value: 3.57e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954  94 RLSLGVVADIDSGRLFGALRTLSERYPLLDVEVLSAAQDDALALLHGGRISLcfGFAGISVNPQE-RFQYVGAESLVATI 172
Cdd:cd08414   1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDV--GFVRPPPDPPGlASRPLLREPLVVAL 78

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15597954 173 SPRHPALQKPgqALYLEELVNVRQILVASCDLP-LADtrpLIAGACWR----------TDSLGTALEMVEAGIG 235
Cdd:cd08414  79 PADHPLAARE--SVSLADLADEPFVLFPREPGPgLYD---QILALCRRagftprivqeASDLQTLLALVAAGLG 147
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 11-177 5.87e-07

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 49.77  E-value: 5.87e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954   11 FLAVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERTHREARPTALARALAPQARMIAEQLAQLQVHALELSQG 90
Cdd:PRK09906   9 FVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRARKIVQE 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954   91 lESRLSLGVVADIDSGRLFGALRTLSERYPLLDVEVLSAAQDDALALLHGGRISLCFGFAGISvNPQERFQYVGAESLVA 170
Cdd:PRK09906  89 -DRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVY-SDEIDYLELLDEPLVV 166


                 ....*..
gi 15597954  171 TISPRHP 177
Cdd:PRK09906 167 VLPVDHP 173
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 19-136 1.34e-06

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 48.69  E-value: 1.34e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954   19 SFSGAARALGRVPSAVSMGIANLEAELGFALFERTHREARPTALARALAPQARMIAEQLAQlqvhALE--LSQGLESRLS 96
Cdd:PRK11139  22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAE----ATRklRARSAKGALT 97

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 15597954   97 lgvvadIDSGRLFGA------LRTLSERYPLLDVEVLSAAQDDALA 136
Cdd:PRK11139  98 ------VSLLPSFAIqwlvprLSSFNEAHPDIDVRLKAVDRLEDFL 137
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 8-63 8.88e-06

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 46.52  E-value: 8.88e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 15597954    8 IELFLAVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERTHREARPTALA 63
Cdd:PRK11013   9 IEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQG 64
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 11-86 1.83e-05

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 45.37  E-value: 1.83e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15597954   11 FLAVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERTHREARPTALARALAP--QARMIAEQLAQLQVHALE 86
Cdd:PRK14997  10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEhcKAMLVEAQAAQDAIAALQ 87
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-120 1.88e-05

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 45.44  E-value: 1.88e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954    1 MNFSSdtIELFLAVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERTHREARPTALARALAPQARMIAEQLAQL 80
Cdd:PRK11233   1 MNFRR--LKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQA 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 15597954   81 QVHALELSQGLESRLSLGVVADIDSGRL-FGALRTLSERYP 120
Cdd:PRK11233  79 QLAVHNVGQALSGQVSIGLAPGTAASSLtMPLLQAVRAEFP 119
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 122-278 2.11e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 44.57  E-value: 2.11e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954 122 LDVEVLSAAQDDalalLHGGRISLCFGFAGISVNPQERFQYVGAESLVATISPRHPaLQKPGQALYLEELVNVRQILVA- 200
Cdd:cd08431  33 LSEEVLGGTWDA----LASGRADLVIGATGELPPGGVKTRPLGEVEFVFAVAPNHP-LAKLDGPLDASAIKQYPAIVVAd 107

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954 201 -SCDLP-----LADTRPLIagacwRTDSLGTALEMVEAGIGWGNFPLSRVAPLLATGRLVRLDFRNTKNElkLPVHAIWL 274
Cdd:cd08431 108 tSRNLPprssgLLEGQDRI-----RVPTMQAKIDAQVLGLGVGYLPRHLAKPELASGELVEKALEDPRPP--QELFLAWR 180


                ....
gi 15597954 275 KNQP 278
Cdd:cd08431 181 KDQR 184
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-60 2.33e-05

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 45.01  E-value: 2.33e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 15597954    3 FSSDTIELFLAVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERTHREARPT 60
Cdd:CHL00180   5 FTLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLT 62
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 1-81 4.15e-05

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 44.29  E-value: 4.15e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954    1 MNFSSDTIELFLAVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERTHREARPTALARALAPQARMIAEQLAQL 80
Cdd:PRK10837   1 MHITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEI 80


                 .
gi 15597954   81 Q 81
Cdd:PRK10837  81 E 81
PRK10341 PRK10341
transcriptional regulator TdcA;
10-289 4.71e-05

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 44.08  E-value: 4.71e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954   10 LFLAVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERTHREARPTALARALAPQARMIAEQLAQLQVHALELSQ 89
Cdd:PRK10341  14 VFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGMSS 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954   90 GLESRLSLGVVADIDSGRLFGALRTLSERYPLLDVEVLSAAQDDALALLHGGRISLCFGfagiSVNPQERFQYVGAE--- 166
Cdd:PRK10341  94 EAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIG----TLSNEMKLQDLHVEplf 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954  167 ----SLVATISprhpalqKPGQ-ALYLEELVNVRQILVASC-----DL--PLADTRPLIAGACwRTDSLGTALEMVEAGI 234
Cdd:PRK10341 170 esefVLVASKS-------RTCTgTTTLESLKNEQWVLPQTNmgyysELltTLQRNGISIENIV-KTDSVVTIYNLVLNAD 241

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 15597954  235 GWGNFPLSRVAPlLATGRlvrldFRNTKNELKLPV---HAIWLKNQPLRKAAQELVGM 289
Cdd:PRK10341 242 FLTVIPCDMTSP-FGSNQ-----FITIPIEETLPVaqyAAVWSKNYRIKKAASVLVEL 293
PBP2_BenM_CatM_CatR cd08445
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 93-235 1.07e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold; This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes of the ortho-pathway required for benzoate catabolism: muconate lactonizing enzyme I, muconolactone isomerase, and catechol 1,2-dioxygenase. CatR normally responds to benzoate and cis,cis-muconate, an inducer molecule, to activate transcription of the catBCA operon, whose gene products convert benzoate to catechol. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176136  Cd Length: 203  Bit Score: 42.21  E-value: 1.07e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954  93 SRLSLGVVADIDSGRLFGALRTLSERYPLLDVEVLSAAQDDALALLHGGRISLCFGFAGISvNPQERFQYVGAESLVATI 172
Cdd:cd08445   1 RTFSIGFVPSTLYGLLPELIRRFRQAAPDVEIELIEMTTVQQIEALKEGRIDVGFGRLRIE-DPAIRRIVLREEPLVVAL 79

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15597954 173 SPRHPALQKPGQaLYLEELVNVRQIL--------VASCDLPLADTRPLIAGACWRTDSLGTALEMVEAGIG 235
Cdd:cd08445  80 PAGHPLAQEKAP-LTLAQLADEPLILypasprpsFADQVLSLFRDHGLRPRVIQEVRELQTALGLVAAGEG 149
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
13-145 1.19e-04

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 43.08  E-value: 1.19e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954   13 AVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERTHREARPTALARALAPQARMIAEQLAQlqvhALE-LSQGL 91
Cdd:PRK15421  12 ALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQ----ALQaCNEPQ 87

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 15597954   92 ESRLSLGVVADIDSGRLFGALRTLSERYPLLDVEVLSAAQDDALALLHGGRISL 145
Cdd:PRK15421  88 QTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDL 141
PRK09801 PRK09801
LysR family transcriptional regulator;
8-124 4.29e-04

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 41.17  E-value: 4.29e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954    8 IELFLAVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERTHREARPTALARALAPQARMIAEQLAQLQVHALEL 87
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 15597954   88 SQGLESRLSLGVVADIDSGRLFGALRTLSERYPLLDV 124
Cdd:PRK09801  91 KTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQV 127
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-257 4.95e-04

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 40.27  E-value: 4.95e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954  94 RLSLGVVADIDSGRLFGALRTLSERYPLLDVEVLSAAQDDALALLHGGRISLCFGFA--GISVNPQERFQYV--GAESLV 169
Cdd:cd08423   1 TLRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFDypVTPPPDDPGLTRVplLDDPLD 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954 170 ATISPRHPALQKPgqALYLEELVNVRQI-----------LVASCDlpLADTRPLIAgacWRTDSLGTALEMVEAGIGWGN 238
Cdd:cd08423  81 LVLPADHPLAGRE--EVALADLADEPWIagcpgspchrwLVRACR--AAGFTPRIA---HEADDYATVLALVAAGLGVAL 153

                       170
                ....*....|....*....
gi 15597954 239 FPLSRVAPLLATGRLVRLD 257
Cdd:cd08423 154 VPRLALGARPPGVVVRPLR 172
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
11-125 6.80e-04

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 40.39  E-value: 6.80e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954   11 FLAVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERTHREARPTALARALAPQAR--MIAEQLAQLQV-HALEL 87
Cdd:PRK03601   9 FLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAEtlMNTWQAAKKEVaHTSQH 88

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 15597954   88 SQglesrLSLGVVADIDSGRLFGALRTLSERYPLLDVE 125
Cdd:PRK03601  89 NE-----LSIGASASLWECMLTPWLGRLYQNQEALQFE 121
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
31-97 1.08e-03

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 39.80  E-value: 1.08e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15597954   31 PSAVSMGIANLEAELGFALFERTHREARPTALARALAPQARMIAEQLAQLQVHALELSQGLESRLSL 97
Cdd:PRK11716   5 PSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSL 71
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-290 1.16e-03

TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176131 [Multi-domain]  Cd Length: 197  Bit Score: 39.05  E-value: 1.16e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954  94 RLSLGVVADIDSGRLFGALRTLSERYPLLDVEVLSAAQDDALALLHGGRISLCFGFAGiSVNPQERFQYVGAESLVATIS 173
Cdd:cd08440   1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEP-EADPDLEFEPLLRDPFVLVCP 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954 174 PRHPALQKPgqALYLEELVNVRQILVASC-------DLPLADtRPLIAGACWRTDSLGTALEMVEAGIGWGNFPlSRVAP 246
Cdd:cd08440  80 KDHPLARRR--SVTWAELAGYPLIALGRGsgvraliDRALAA-AGLTLRPAYEVSHMSTALGMVAAGLGVAVLP-ALALP 155

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
gi 15597954 247 LLATGRLVRLDFrnTKNELKLPVHAIWLKNQPLRKAAQELVGML 290
Cdd:cd08440 156 LADHPGLVARPL--TEPVVTRTVGLIRRRGRSLSPAAQAFLDLL 197
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 94-289 1.20e-03

The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of N2 fixing bacteria, and synthesis of virulence factors, to a name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 39.06  E-value: 1.20e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954  94 RLSLGVVADIDSGRLFGALRTLSERYPLLDVEVLSAAQDDALALLHGGRISLCFGFaGISVNPQERFQYVGAESLVATIS 173
Cdd:cd08412   1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTY-DLDLPEDIAFEPLARLPPYVWLP 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954 174 PRHPALQKPgqALYLEELVNVRQILVascDLPLADT-----------RPLIAGacwRTDSLGTALEMVEAGIGWGNFPLS 242
Cdd:cd08412  80 ADHPLAGKD--EVSLADLAAEPLILL---DLPHSREyflslfaaaglTPRIAY---RTSSFEAVRSLVANGLGYSLLNDR 151

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*...
gi 15597954 243 RVAPL-LATGRLVRLDFRNTKNELKLPVhaIWLKNQPLRKAAQELVGM 289
Cdd:cd08412 152 PYRPWsYDGKRLVRRPLADPVPPLRLGL--AWRRGARLTRAARAFVDF 197
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
7-55 3.15e-03

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 38.59  E-value: 3.15e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 15597954    7 TIELFLAVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERTHR 55
Cdd:PRK10632   6 RMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTR 54
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 112-290 3.69e-03

C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 37.86  E-value: 3.69e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954 112 LRTLSERYPLLDVEVLSAAQDDALALLHGGRISLcfGF-AGISVNPQERFQYVGAESLVATISPRHPALQKpgQALYLEE 190
Cdd:cd08420  19 LARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDL--GLvEGPVDHPDLIVEPFAEDELVLVVPPDHPLAGR--KEVTAEE 94

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954 191 LVNVRQIL--VASCdlpladTRP----LIAGACWRTDSLGTALEM---------VEAGIGWGNFPLSRVAPLLATGRLVR 255
Cdd:cd08420  95 LAAEPWILrePGSG------TREvferALAEAGLDGLDLNIVMELgsteaikeaVEAGLGISILSRLAVRKELELGRLVA 168

                       170       180       190
                ....*....|....*....|....*....|....*
gi 15597954 256 LDFRNTknELKLPVHAIWLKNQPLRKAAQELVGML 290
Cdd:cd08420 169 LPVEGL--RLTRPFSLIYHKDKYLSPAAEAFLEFL 201
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-55 4.48e-03

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 38.09  E-value: 4.48e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 15597954    1 MNFSSDTIELFLAVLDRGSFSGAARALGRVPSAVSMGIANLEAELGFALFERTHR 55
Cdd:PRK15092   9 INLDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGR 63
PRK12680 PRK12680
LysR family transcriptional regulator;
23-237 4.63e-03

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 38.06  E-value: 4.63e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954   23 AARALGRVPsAVSMGIANLEAELGFALFERTHREARP-TALARALAPQARMIAEQLAQLQVHALELSQGLESRLSLGVVA 101
Cdd:PRK12680  23 AARVHATQP-GLSKQLKQLEDELGFLLFVRKGRSLESvTPAGVEVIERARAVLSEANNIRTYAANQRRESQGQLTLTTTH 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954  102 DIDSGRLFGALRTLSERYPLLDVEVLSAAQDDALALLHGGRISLCF-------GFAGISVnPQERFQYVgaeslvaTISP 174
Cdd:PRK12680 102 TQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIvstaggePSAGIAV-PLYRWRRL-------VVVP 173

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15597954  175 RHPALQKPGQALYLEELVNVRQILVASCDLPLADTRPLIAGACWRTDSLGTALEM------VEAGIGWG 237
Cdd:PRK12680 174 RGHALDTPRRAPDMAALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDAdliktyVRAGLGVG 242
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 219-279 5.69e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 37.03  E-value: 5.69e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15597954 219 RTDSLGTALEMVEAGIGWGNFPLSRVAPLLATGRLVRL--DFRNTknelKLPVHAIWLKNQPL 279
Cdd:cd08422 128 VVNDGEALRAAALAGLGIALLPDFLVAEDLASGRLVRVlpDWRPP----PLPIYAVYPSRRHL 186
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 94-286 5.97e-03

The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176129 [Multi-domain]  Cd Length: 197  Bit Score: 37.15  E-value: 5.97e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954  94 RLSLGVVADIDSGRLFGALRTLSERYPLLDVEVL---SAAQDDALAllhGGRISLcfgfaGISVNP--QERFQY--VGAE 166
Cdd:cd08438   1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVeygGKKVEQAVL---NGELDV-----GITVLPvdEEEFDSqpLCNE 72

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597954 167 SLVATISPRHPALQKPgqALYLEELVNVRQILVAScDLPLADtrpLIAGAC----------WRTDSLGTALEMVEAGIGW 236
Cdd:cd08438  73 PLVAVLPRGHPLAGRK--TVSLADLADEPFILFNE-DFALHD---RIIDACqqagftpniaARSSQWDFIAELVAAGLGV 146

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|.
gi 15597954 237 GNFPLSRVAPLLATG-RLVRLDFRNTKNELKLpvhaIWLKNQPLRKAAQEL 286
Cdd:cd08438 147 ALLPRSIAQRLDNAGvKVIPLTDPDLRWQLAL----IWRKGRYLSHAARAW 193
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH